The classification of bamboos based on floral morphology and reproductive characters is very hard due to erratic flowering behavior and unusually long reproductive cycle. The application of reliable and effective DNA molecular markers is highly essential to address this problem. In the present investigation, inter-simple sequence repeats (ISSR) markers were employed to study phylogenetic relationship of 15 different bamboos of North-East India. The 10 ISSR primers generated 116 polymorphic loci or scorable bands with average of 11.6 bands per primer. The genetic similarity coefficient ranged from 0.41-0.76 showing high genetic polymorphism among different bamboo species. The phylogenetic tree constructed based on genetic similarity matrix revealed genetic proximity of endemic Bambusa mizorameana to other five Dendrocalamus species by clustering into a single group, while Dendrocalamus manipureanus segregated from the cluster indicating its genetic divergent character. Except for Schizotachyum fuchsianum, the three Schizotachyum species viz., S. dullooa, S. pergracile and S. munroi exhibited close genetic affinity by grouping into a single minor clade. Principal coordinates analysis (PCoA) showed distribution of different bamboos species in the plot in accordance to unweighted pair-group method with arithmetic average (UPGMA) cluster analysis. Genetic relationship of 15 different bamboos as revealed from the dendrogram and PCoA analysis reasonably conformed to traditional system of classification though slight disagreement existed. This is the first report on the successful use of ISSR markers in the phylogenetic and genetic variation studies of 15 important bamboos of the region including the endemic bamboo species of B. mizorameana, B. manipureana, D. sikkimensis and D. manipureanus.